A qualitative evaluation of the published oligonucleotides specific for the 16S rRNA gene sequences of the ammonia-oxidizing bacteria

Systematic and Applied Microbiology

Volumn 21, Issue 1, 1998, Pages 72-88

  Utåker, Janne Beate ^a   Nes, Ingolf F ^a  

^a NONE

Author keywords

16S rRNA; Ammonia oxidizing bacteria; Nitrifying bacteria; PCR; Phylogeny; Specific oligonucleotides

Indexed keywords

AMMONIA; OLIGONUCLEOTIDE; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIUM CULTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PHYLOGENY; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; NITROSOMONADALES; NITROSOSPIRA; PROKARYOTA; PROTEOBACTERIA;

EID: 2642611982     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0723-2020(98)80010-6     Document Type: Article

References (44)

1. AMANN, R. I., LUDWIG, W., SCHLEIFER, K.-H.: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 59, 143-169 (1995).
2. AMANN, R., SNAIDR, J., WAGNER, M., LUDWIG, W., SCHLEIFER, K.-H.: In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178, 3496-3500 (1996).
3. BROSIUS, J., PALMER, M. L., KENNEDY, P. J., NOLLER, H. F.: Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Nad. Acad. Sci. USA, 75, 4801-4805 (1978).
4. CHANDLER, D. P., SCHRECKHISE, R. W., SMITH, J. L., BOLTON JR., H.: Electroelution to remove humic compounds from soil DNA and RNA extracts. J. Microbiol. Methods, 28, 11-19 (1997).
5. DONALDSON, J. M., HENDERSON, G. S.: A dilute medium to determine population size of ammonium oxidizers in forest soils. Soil. Sci. Soc. Am. 53, 1608-1611 (1989).
6. FELSENSTEIN, J.: Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791 (1985).
7. FELSENSTEIN, J.: PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle (1993).
8. HASTINGS, R. C., CECCHERINI, M. T., MICLAUS, N., SAUNDERS, J. R., BAZZICALUPO, M., MCCARTHY, A. J.: Direct molecular biological analysis of ammonia oxidizing bacteria populations in cultivated soil plots treated with swine manure. FEMS Microb. Ecol., 23, 45-54 (1997).
9. HIORNS, W. D., HASTINGS, R. C., HEAD, I. M., MCCARTHY, A. J., SAUNDERS, J. R., PICKUP, R. W., HALL, G. H.: Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment. Microbiology, 141, 2793-2800 (1995).
10. HEAD, I. M., HIORNS, W. D., EMBLEY, T. M., MCCARTHY, A. J., SAUNDERS, J. R.: The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J. Gen. Microbiol., 139, 1147-1153 (1993).
11. HOVANEC, T. A., DELONG, E. F.: Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl. Environ. Microbiol., 62, 2888-2896 (1996).
12. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY: Validation of the publication of new names and new combinations previously effectively published outside the IJSB, List No. 54, Int. J. Syst. Bacteriol., 45, 619-620 (1995).
13. JIANG, Q. Q.: Nitrosospira from terrestrial environments, its urease activity and nitrous oxide production, Doctor Scientarum Thesis 1996:21, Agricultural University of Norway, (1996).
14. KIMURA, M.: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120 (1980).
15. KOOPS, H. P., HARMS, H.: Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria. Arch. Microbiol., 141, 214-218 (1985).
16. KOPCYNSKI, E. D., BATESON, M. M., WARD, D. M.: Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol., 60, 746-748 (1994).
17. KOWALCHUK, G. A., STEPHEN, J. R., DE BOER, W., PROSSER, J. I., EMBLEY, T. M., WOLDENDORP, J. D.: Analysis of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl. Environ. Microbiol., 63, 1489-1497 (1997).
18. MCCAIG, A. E., EMBLEY, T. M., PROSSER, J. I.: Molecular analysis of enrichment cultures of marine ammonia oxidizers. FEMS Microbiol. Lett. 120, 363-368 (1994).
19. MOBARRY, B. K., WAGNER, M., URBAIN, V., RITTMANN, B. E., STAHL, D. A.: Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol., 62, 2156-2162 (1996).
20. MOBARRY, B. K., WAGNER, M., URBAIN, V., RITTMANN, B. E., STAHL, D. A.: Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria (erratum). Appl. Environ. Microbiol., 63, 815 (1997).
21. PAGE, R., D. M.: TreeView - Tree drawing software for Apple Macintosh and Microsoft Windows. Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, UK (http:// taxonomy.zoology.gla.ac.ult/rod/treeview.html) (1996).
22. PEARSON, W. R., LIPMAN, D. J.: Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85, 2444-2448 (1988).
23. POMMERENING-RÖSER, A., RATH, G., KOOPS, H.-P.: Phylogenetic diversity within the genus Nitrosomonas. System. Appl. Microbiol. 19, 344-351 (1996).
24. ROTTHAUWE, J.-H., DE BOER, W., LISACK, W.: Comparative analysis of gene sequences encoding ammonia monooxygenase of Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71. FEMS Microbiol. Lett., 133, 131-135 (1995).
25. SAITOU, N., NEI, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425 (1987).
26. SCHMIDT, E. L., BELSER, L. W: Autotrophic nitrifying bacteria, pp. 159-177. In: Methods of soil analysis, part 2, Microbiological and biochemical Properties, Madison, SSSA Book Series, no. 5 (1994).
27. SCHMIDT, I., BOCK, E.: Anaerobic ammonia oxidation with nitrogen dioxide by Nitrosomonas eutropha. Arch. Microbiol., 167, 106-111 (1997).
28. SINIGALLIANO, C. D., KUHN, D. N., JONES, R. D.: Amplification of the amoA gene from diverse species of ammonium-oxidizing bacteria and from an indigenous bacterial population from sea water. Appl. Environ. Microbiol., 61, 2702-2706 (1995).
29. SMITH, T., WATERMAN, M. S.: Identification of common molecular subsequences, J. Mol. Biol., 147, 195-197 (1981). Basis for the MPSearch program with the address http://www. dna.affrc.go.jp:10082/htdocs/MPsrch/index.html.
30. STAHL, D. A., AMANN, R.: Development and application of nucleic acid probes, pp. 205-248. In: Nucleic Acid Techniques in Bacterial Systematics (STACKEBRANDT, E., GOODFELLOW, M. eds.) West Sussex, England, Wiley & Sons Ltd. 1991.
31. STEPHEN, J. R., MCCAIG, A. E., SMITH, Z., PROSSER, J. I., EMBLEY, T. M.: Molecular diversity of soil and marine 16S rRNA gene sequences related to β-subgroup ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 62, 4147-4154 (1996).
32. TESKE, A., ALM, E., REGAN, J. M., TOZE, S., RITTMANN, B. E., STAHL, D. A.: Evolutionary relationships among ammonia-and nitrite-oxidizing bacteria. J. Bacteriol. 176, 6623-6630 (1994).
33. THOMPSON, J. D., HIGGINS, D. G., GIBSON, T. J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680 (1994).
34. TRUPER, H. G., DE'CLARI, L.: Taxonomic note: necessary correction of specific epithets formed as substantives (nouns) "in apposition". Int. J. Syst. Bacteriol., 47, 908-909 (1997).
35. UTÅKER, J. B., BAKKEN, L. R., JIANG, Q. Q. & NES, I. F.: Phylogenetic analysis of seven new isolates of the highly related ammonia-oxidizing bacteria based on 16S rRNA gene sequences. System. Appl. Microbiol., 18, 549-559 (1995).
36. VOYTEK, M. A., WARD, B. B.: Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl. Environ. Microbiol. 61, 1444-1450 (1995a).
37. VOYTEK, M. A., WARD, B. B.: Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR (erratum). Appl. Environ. Microbiol., 61, 2811 (1995b).
38. WAGNER, M., AMANN, R., LEMMER, H., SCHLEIFER, K.-H.: Probing activated sludge with oligonucleotides specific for Proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol., 59, 1520-1525 (1993).
39. WAGNER, M., RATH, G., AMANN, R., KOOPS, H.-P., SCHLEIFER, K.-H.: In situ identification of ammonia-oxidizing bacteria. System. Appl. Microbiol., 18, 251-264 (1995).
40. WARD, B. B., VOYTEK, M. A., WITZEL, K.-P.: Phylogenetic diversity of natural populations of ammonia oxidizers investigated by specific PCR amplification. Microb. Ecol., 33, 87-96 (1997).
41. WARD, B. B.: Personal communication: The correct sequence for probe NitC is 5′-AGCTACGTTACCAAGCCC-3′, and the correct sequence for probe NitF is 5′-AGCTACGTTACCAAGTCCGT-3′.
42. WATSON, S. W., BOCK, E., HARMS, H., KOOPS, H. P., HOOPER, A. B.: Ammonia-oxidizing bacteria, pp. 1818-1834. In: Bergey's Manual of Systematic Bacteriology (J. T. STANLEY, M. P. BRYANT, N. PFENNIG, J. G. HOLT eds.), vol. III, Williams & Wilkins, Baltimore, USA (1989).
43. WOESE, C. R., WEISBURG, W. G., PASTER, B. J., HAHN, C. M., TANNER, R. S., KRIEG, N. R., KOOPS, H.-P., STACKEBRANDT, E.: The phylogeny of the purple bacteria: the beta subdivision. Syst. Appl. Microbiol., 5, 327-336 (1984).
44. WOESE, C. R., WEISBURG, W. G., HAHN, C. M., PASTER, B. J., ZABLEN, L. B., LEWIS, B. J., MACKE, T. J., LUDWIG, W., STACKEBRANDT, E.: The phylogeny of the purple bacteria: the gamma subdivision. Syst. Appl. Microbiol., 6, 25-33 (1985).